MiTools

MiTools: yet another Next Generation Sequencing (NGS) data processing tool (based on MiLib)

Installation / Download

Using Homebrew on Mac OS X or Linux (linuxbrew)

brew tap milaboratory/all
brew install mitools

or just

brew install milaboratory/all/mitools

to upgrade already installed MiTools to the newest version:

brew update
brew upgrade mitools

Manual install (any OS)

• download latest MiTools version from release page
• unzip the archive
• add resulting folder to your PATH variable
  • or add symbolic link for mitools script to your bin folder
  • or use MiTools directly by specifying full path to the executable script

Requirements

• Any OS with Java support (Linux, Windows, Mac OS X, etc..)
• Java 1.7 or higher

Usage

Cutting input fastq file to specified read length:

mitools cut -l 50 input.fastq.gz output.fastq.gz

Reverse-complement all reads:

mitools rc input.fastq.gz output.fastq.gz

Merge-overlap paired-end reads (like PEAR but works better in our experience; fast - based on bitap algorithm):

mitools merge input_R1.fastq.gz input_R2.fastq.gz output.fastq.gz

Split input file into chunks of 1M reads:

mitools split -c 1000000 input.fastq.gz output_{P}.fastq.gz

will produce output_0.fastq.gz, output_1.fastq.gz, ... files.

See mitools -h for available command paramenters and other useful actions.

Documentation

See output of

mitools -h

for available actions.

License

Copyright 2016 MiLaboratory.com

Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at

   http://www.apache.org/licenses/LICENSE-2.0

Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.